Skip to main content
SpringerLink
Log in

A General Reconfigurable Architecture for the BLAST Algorithm

  • Published:
The Journal of VLSI Signal Processing Systems for Signal, Image, and Video Technology Aims and scope Submit manuscript

Abstract

The process of DNA sequence matching and database search is one of the major problems of the bioinformatics community. Major scientific efforts to address this problem have provided algorithms and software tools for molecular biologists since the early 1970s. At the algorithmic and software level BLAST is by far the most popular tool. It has been developed and continues to be maintained and distributed by the NCBI organization. The BLAST algorithm and software is computationally very intensive and as a result several computer vendors use it as a benchmark. On the other hand no systematic approach for hardware speedup of BLAST and its variants for different query and database size has been reported to date. In this paper we present our architecture that implements the BLAST algorithm for all of its major versions, and for any size of database and query. The system has been fully designed and partially implemented with reconfigurable logic. It consists of software and hardware parts and achieves a speedup of several times up to thousands of times vs general purpose computers.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. P. G. Higgs and T. K. Attwood, “Bioinformatics And Molecular Evolution,” Blackwell, 2005.

  2. E. Sotiriades, C. Kozanitis and A. Dollas, “FPGA based Architecture of DNA Sequence Comparison and Database Search,” in Proceedings 20th International Parallel and Distributed Processing Symposium, IPDPS 2006, p. 193., at the 13th Reconfigurable Architectures Workshop (RAW 2006), Rhodes, Greece, 25–29 April, 2006

  3. E. Sotiriades, C. Kozanitis and A. Dollas, “Some Initial Results on Hardware BLAST Acceleration with a Reconfigurable Architecture.” in Proceedings 20th International Parallel and Distributed Processing Symposium, IPDPS 2006, p. 251, at the 5th IEEE International Workshop on High Performance Computational Biology (HiCOMB2006), Rhodes, Greece, 25–29 April, 2006.

  4. E. Sotiriades, C. Kozanitis, G. Chrysos and A. Dollas, “Rapid Phototyping of a System-on-a-Chip for the BLAST Algorithm Implementation,” in Proceedings, 17th International IEEE Workshop on Rapid System Prototyping RSP-2006, pp. 223–229, Computer Society, Chania, Greece, 14–16 June, 2006.

  5. E. Sotiriades, C. Kozanitis and A. Dollas, “A Generic Reconfigurable and Fixed Architecture for BLAST Algorithm Implementation,” Microprocessor and Hardware Laboratory Technical Report, 2005.

  6. S. B. Needleman and C. D.Wunsch, “A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins,” J. Mol. Biol., vol. 48, 1970, pp. 443–453.

    Article  Google Scholar 

  7. T. F. Smith and M. S. Waterman, “Identification Of Common Molecular Subsequences,” J. Mol. Biol., vol. 147, 1981, pp. 195–197.

    Article  Google Scholar 

  8. W. Pearson and D. Lipman, “Improved tools for biological sequence analysis,” Proc. Natl. Acad. Sci U S A, vol. 85, 1988, pp. 2444–2448.

    Article  Google Scholar 

  9. S. Altschul et al., “Basic Local Alignment Search Tool,” J. Mol. Biol., vol. 215, 1990, pp. 403–410.

    Google Scholar 

  10. C. P. Sosa et al., “Some Practical Suggestions for Performing NCBI BLAST Benchmarks on a pSeries ™ 690 System,” available at http://www.redbooks.ibm.com/abstracts/redp0437.html?.

  11. R. Radahakrishnan, R. Ali, G. Kochhar, K. Chadalavada and R. Rajagopalan, “Performance Characterization of BLAST on 32-bit and 64-bit Dell PowerEdge Servers,” Dell Power Solutions, February 2005.

  12. D. Hoang et al., “FPGA Implementation of Systolic Sequence Alignment,” in Proceedings of the 2nd International Workshop on Field-Programmable Logic and Applications, Lecture Notes in Computer Science, vol. 705, 1992, pp. 183–191.

  13. D. Hoang, “Searching Genetic Databases on Splash 2,” in Proceedings IEEE Workshop on FPGAs for Custom Computing Machines (FCCM), 1993, pp. 185–191.

  14. S. Guccione and Eric Keller, “Gene Matching Using Jbits,” in Proceedings of the 12th International Conference on Field-Programmable Logic and Applications, Lecture Notes In Computer Science, vol. 2438, 2002, pp. 1168–1171.

  15. K. Puttegowda et al., “A Run-Time Reconfigurable System for Gene-Sequence Searching,” in Proceedings 16th International Conference on VLSI Design, New Delhi, 2003, pp. 561–566.

  16. T. Oliver, B. Schmidt and D. Maskel, “Reconfigurable Architectures for Bio-sequence Database Scanning on FPGAs,” IEEE Trans. Circuits Syst. II, vol. 52, no. 12, 2005, pp. 851–855.

    Article  Google Scholar 

  17. K. Muriki, K. Underwood and R Sass, “RC-BLAST: Towards an open source hardware implementation,” in Proceedings of the International Workshop on High Performance Computational Biology, Denver, 2005.

  18. M. C. Herbordt, J. Model, Y. Gu, B. Sukhwani, and T. VanCourt, “Single Pass, BLAST-Like, Approximate String Matching on FPGAs,” in 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM’06), 2006, pp. 217–226.

  19. C. Chang, “BLAST Implementation on BEE2,” University of California at Berkeley, California, 2004.

    Google Scholar 

  20. K. Compton, S. Hauck, “Reconfigurable Computing: A Survey of Systems and Software,” ACM Comput. Surv., vol. 34, no. 2, 2002, pp. 171–210.

    Article  Google Scholar 

  21. J. Meidanis and J. C. Setubal, “Introduction to Computational Molecular Biology,” PWS, 1997.

  22. D. Lavenier, L. Xinchun, and G. Georges, “Seed-based Genomic Sequence Comparison using a FPGA/FLASH Accelerator,” in Proceedings of IEEE International Conference on Field Programmable Technology (FPT ‘06), 2006, pp. 41–48.

  23. P. Krishnamurthy, J. Buhler, R. Chamberlain, M. Franklin, K. Gyang and J. Lancaster, “Biosequence Similarity Search on the Mercury System,” in Proc. of the IEEE 15th Int’l Conf. on Application-Specific Systems, Architectures and Processors, September 2004, pp. 365–375.

  24. J. Lancaster, J. Buhler, R. Chamberlain, “Acceleration of Ungapped Extension in Mercury BLAST,” in 7th workshop on media and streaming processors, Barcelona, Spain, November 12, 2005.

Download references

Author information

Authors and Affiliations

  1. Department of Electronic and Computer Engineering, Technical University of Crete, 73100, Chania, Crete, Greece

    Euripides Sotiriades & Apostolos Dollas

Authors
  1. Euripides Sotiriades
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Apostolos Dollas
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Euripides Sotiriades.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Sotiriades, E., Dollas, A. A General Reconfigurable Architecture for the BLAST Algorithm. J VLSI Sign Process Syst Sign Im 48, 189–208 (2007). https://doi.org/10.1007/s11265-007-0069-2

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11265-007-0069-2

Keywords

Search

Navigation